Hybrid Genome Assembly of Berkeleyomyces rouxiae, an Emerging Cannabis Fungal Pathogen Causing Black Root-Rot in an Aeroponic Facility

doi: 10.1094/PDIS-11-22-2690-RE.

Online ahead of print.


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Chris Dumigan et al.

Plant Dis.



The resurged interest in cultivation of Cannabis sativa has presented an array of new challenges. Among them are the difficult to control pests and pathogens that infect cannabis plants. The limited methods for disease control available to cannabis growers necessitates early detection of plant pathogens, something that molecular techniques such as DNA sequencing has greatly improved. This study reports for the first time the fungal plant-pathogen Berkeleyomyces rouxiae causing black root rot in drug-type cannabis. Aeroponically grown cannabis plants at a licenced production facility in Cranbrook BC, Canada, rapidly displayed root discolouration and rot symptoms despite testing negative for all commercially available pathogen tests. Developing sequencing-based disease diagnostics requires genomic information, therefore this study presents the first whole genome sequence of the multi-host, widespread black root-rot pathogen, Berkeleyomyces rouxiae. Hybrid genome assembly using Oxford Nanopore long-reads and Illumina short-reads yielded a genome size of 28.2 Mb represented over 404 contigs with an N50 of 267 kb. Genome annotation predicted 6960 protein-coding genes with 59,477 functional annotations. The availability of this genome will assist in sequence-based diagnostic development, comparative genomics, and taxonomic resolution of this globally important plant pathogen.


Berkeleyomyces; Black root rot; Cannabis; Causal Agent; Fungi; Genome; Thielaviopsis.

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